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Merge pull request #8512 from jmchilton/page_format

Browse Source 
Markdown-based Galaxy Pages.
This commit is contained in:
Marius van den Beek
2019-12-17 22:37:21 +02:00
committed by GitHub
parent 4704610ef6 fbd508ada2
commit c10a434fcc
43 changed files with 1269 additions and 196 deletions
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client/galaxy/scripts/bundleEntries.js
+1
View File
@@ -94,6 +94,7 @@ export { mountMakoTags } from "components/Tags";
export { mountJobMetrics } from "components/JobMetrics";
export { mountJobParameters } from "components/JobParameters";
export { mountWorkflowEditor } from "components/Workflow/Editor/mount";
export { mountPageDisplay } from "components/PageDisplay";
// Used in common.mako
export { default as store } from "storemodern";
client/galaxy/scripts/components/DataDialog/DataDialog.test.js
+28 -14
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@@ -1,10 +1,10 @@
import { mount } from "@vue/test-utils";
import DataDialog from "./DataDialog.vue";
import SelectionDialog from "components/SelectionDialog/SelectionDialog.vue";
import { __RewireAPI__ as rewire } from "./DataDialog";
import { Model } from "./model.js";
import { UrlTracker } from "./utilities.js";
import { Services } from "./services";
import Vue from "vue";
import { mount, createLocalVue } from "@vue/test-utils";
const mockOptions = {
callback: () => {},
@@ -80,9 +80,9 @@ describe("services/Services:isDataset", () => {
expect(services.isDataset({ history_content_type: "dataset" })).to.equals(true);
expect(services.isDataset({ history_content_type: "xyz" })).to.equals(false);
expect(services.isDataset({ type: "file" })).to.equals(true);
expect(services.getRecord({ hid: 1, history_content_type: "dataset" }).isDataset).to.equals(true);
expect(services.getRecord({ hid: 2, history_content_type: "xyz" }).isDataset).to.equals(false);
expect(services.getRecord({ type: "file" }).isDataset).to.equals(true);
expect(services.getRecord({ hid: 1, history_content_type: "dataset" }).isLeaf).to.equals(true);
expect(services.getRecord({ hid: 2, history_content_type: "xyz" }).isLeaf).to.equals(false);
expect(services.getRecord({ type: "file" }).isLeaf).to.equals(true);
});
});
@@ -137,18 +137,32 @@ describe("DataDialog.vue", () => {
};
beforeEach(() => {
rewire.__Rewire__("Services", mockServices);
rewire.__Rewire__("getGalaxyInstance", () => {
root: "root";
});
const localVue = createLocalVue();
wrapper = mount(DataDialog, {
propsData: mockOptions
propsData: mockOptions,
attachToDocument: true,
localVue
});
});
it("loads correctly, shows datasets and folders", async () => {
expect(wrapper.find(":first-child div").classes()).contain("data-dialog-modal");
expect(wrapper.find(".fa-spinner").text()).to.equals("");
expect(wrapper.contains(".fa-spinner")).to.equals(true);
await Vue.nextTick();
expect(wrapper.findAll(".fa-folder").length).to.equals(2);
expect(wrapper.findAll(".fa-file-o").length).to.equals(2);
it("loads correctly, embeds a SelectionDialog", async () => {
expect(wrapper.find(SelectionDialog).is(SelectionDialog)).to.equals(true);
// Cannot get nested slot templates to render into the wrapper
/// Lots of open issues around this
/// ... Maybe because named slots have many issues
// - https://github.com/vuejs/vue-test-utils/issues?utf8=%E2%9C%93&q=is%3Aissue+is%3Aopen+slot
// ... Maybe because it is a modal and no longer inside the template DOM element?
// - https://github.com/vuejs/vue-test-utils/issues/1333
// expect(wrapper.find(".fa-spinner").text()).to.equals("");
// expect(wrapper.contains(".fa-spinner")).to.equals(true);
// await Vue.nextTick();
// expect(wrapper.findAll(".fa-folder").length).to.equals(2);
// expect(wrapper.findAll(".fa-file-o").length).to.equals(2);
// SelectionDialog DOM properties are tested now in SelectionDialog.test.js however.
});
});
client/galaxy/scripts/components/DataDialog/DataDialog.vue
+30 -46
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@@ -1,10 +1,14 @@
<template>
<b-modal modal-class="data-dialog-modal" v-if="modalShow" visible ok-only ok-title="Close" :static="modalStatic">
<template v-slot:modal-header>
<selection-dialog
:errorMessage="errorMessage"
:optionsShow="optionsShow"
:modalShow="modalShow"
:hideModal="() => (modalShow = false)"
>
<template v-slot:search>
<data-dialog-search v-model="filter" />
</template>
<b-alert v-if="errorMessage" variant="danger" show v-html="errorMessage" />
<div v-else>
<template v-slot:options>
<data-dialog-table
v-if="optionsShow"
:items="items"
@@ -13,35 +17,30 @@
@clicked="clicked"
@load="load"
/>
<div v-else><span class="fa fa-spinner fa-spin" /> <span>Please wait...</span></div>
</div>
<template v-if="!errorMessage" v-slot:modal-footer>
<div class="w-100">
<b-btn size="sm" class="float-left" v-if="undoShow" @click="load()">
<div class="fa fa-caret-left mr-1" />
Back
</b-btn>
<b-btn
v-if="multiple"
size="sm"
class="float-right ml-1"
variant="primary"
@click="finalize"
:disabled="!hasValue"
>
Ok
</b-btn>
<b-btn size="sm" class="float-right" @click="modalShow = false"> Cancel </b-btn>
</div>
</template>
</b-modal>
<template v-slot:buttons>
<b-btn size="sm" class="float-left" v-if="undoShow" @click="load()">
<div class="fa fa-caret-left mr-1" />
Back
</b-btn>
<b-btn
v-if="multiple"
size="sm"
class="float-right ml-1"
variant="primary"
@click="finalize"
:disabled="!hasValue"
>
Ok
</b-btn>
</template>
</selection-dialog>
</template>
<script>
import Vue from "vue";
import BootstrapVue from "bootstrap-vue";
import DataDialogSearch from "./DataDialogSearch.vue";
import DataDialogTable from "./DataDialogTable.vue";
import SelectionDialogMixin from "components/SelectionDialog/SelectionDialogMixin";
import { UrlTracker } from "./utilities.js";
import { Model } from "./model.js";
import { Services } from "./services.js";
@@ -49,15 +48,8 @@ import { Services } from "./services.js";
Vue.use(BootstrapVue);
export default {
components: {
"data-dialog-search": DataDialogSearch,
"data-dialog-table": DataDialogTable
},
mixins: [SelectionDialogMixin],
props: {
callback: {
type: Function,
required: true
},
multiple: {
type: Boolean,
default: false
@@ -95,8 +87,7 @@ export default {
modalShow: true,
optionsShow: false,
undoShow: false,
hasValue: false,
oldnewItems: false
hasValue: false
};
},
created: function() {
@@ -114,7 +105,7 @@ export default {
formatRows() {
for (const item of this.items) {
let _rowVariant = "active";
if (item.isDataset) {
if (item.isLeaf) {
_rowVariant = this.model.exists(item.id) ? "success" : "default";
}
Vue.set(item, "_rowVariant", _rowVariant);
@@ -122,7 +113,7 @@ export default {
},
/** Collects selected datasets in value array **/
clicked: function(record) {
if (record.isDataset) {
if (record.isLeaf) {
this.model.add(record);
this.hasValue = this.model.count() > 0;
if (this.multiple) {
@@ -166,10 +157,3 @@ export default {
}
};
</script>
<style>
.data-dialog-modal .modal-body {
max-height: 50vh;
height: 50vh;
overflow-y: auto;
}
</style>
client/galaxy/scripts/components/DataDialog/services.js
+1 -1
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@@ -53,7 +53,7 @@ export class Services {
getRecord(record) {
record.details = record.extension || record.description;
record.time = record.update_time || record.create_time;
record.isDataset = this.isDataset(record);
record.isLeaf = this.isDataset(record);
if (record.time) {
record.time = record.time.substring(0, 16).replace("T", " ");
}
client/galaxy/scripts/components/Markdown/Markdown.vue
+7 -2
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@@ -16,6 +16,7 @@ import MarkdownIt from "markdown-it";
import JOB_STATES_MODEL from "mvc/history/job-states-model";
import HDCAModel from "mvc/history/hdca-model";
import HDCAListItemEdit from "mvc/history/hdca-li-edit";
import HDCAListItem from "mvc/history/hdca-li";
const FUNCTION_CALL_LINE_TEMPLATE = /\s*(\w+)\s*\((\s*\w+\s*=\s*\w+\s*)\)\s*/m;
@@ -140,6 +141,10 @@ export default {
props: {
markdownConfig: {
type: Object
},
readOnly: {
type: Boolean,
default: true
}
},
data() {
@@ -190,8 +195,8 @@ export default {
jobStateSummariesCollection.historyId = hdca["history_id"];
jobStateSummariesCollection.monitor();
jobStateSummariesCollection.trackModel(hdcaModel);
return new HDCAListItemEdit.HDCAListItemEdit({
const viewClass = this.readOnly ? HDCAListItem.HDCAListItemView : HDCAListItemEdit.HDCAListItemEdit;
return new viewClass({
model: hdcaModel,
el: $(el),
linkTarget: "galaxy_main",
client/galaxy/scripts/components/Markdown/MarkdownEditor.vue
+172 -6
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@@ -1,9 +1,87 @@
<template>
<textarea class="markdown-textarea" id="workflow-report-editor" v-model="input" @input="update"> </textarea>
<div style="display: flex; flex: 1; flex-direction: column">
<ul class="galaxymark-toolbar" ref="menu" v-if="toolbar">
<li>
<a
href="#"
class="fa-2x fa fa-file"
@click="selectDataset"
v-b-tooltip.hover
title="Insert Dataset"
></a>
</li>
<li>
<a
href="#"
class="fa-2x fa fa-folder"
@click="selectDatasetCollection"
v-b-tooltip.hover
title="Insert Dataset Collection"
></a>
</li>
<li>
<a
href="#"
class="fa-2x fa fa-sitemap fa-rotate-270"
@click="selectWorkflow"
v-b-tooltip.hover
title="Inseert Workflow Preview"
></a>
</li>
<li>
<a
href="#"
class="fa-2x fa fa-image"
@click="selectDatasetForImage"
v-b-tooltip.hover
title="Insert Dataset as an Image"
></a>
</li>
<li>
<a
href="#"
class="fa-2x fa fa-question"
@click="showMarkdownHelp"
v-if="showMarkdownHelp != null"
v-b-tooltip.hover
title="Show Galaxy Markdown Help"
></a>
</li>
</ul>
<textarea class="markdown-textarea" id="workflow-report-editor" v-model="input" @input="update" ref="editor">
</textarea>
</div>
</template>
<script>
import _ from "underscore";
import Vue from "vue";
import BootstrapVue from "bootstrap-vue";
Vue.use(BootstrapVue);
import { dialog, datasetCollectionDialog, workflowDialog } from "utils/data";
const FENCE = "```";
// https://stackoverflow.com/questions/11076975/insert-text-into-textarea-at-cursor-position-javascript
function _insertAtCursor(myField, myValue) {
//IE support
if (document.selection) {
myField.focus();
var sel = document.selection.createRange();
sel.text = myValue;
}
//MOZILLA and others
else if (myField.selectionStart || myField.selectionStart == "0") {
var startPos = myField.selectionStart;
var endPos = myField.selectionEnd;
myField.value =
myField.value.substring(0, startPos) + myValue + myField.value.substring(endPos, myField.value.length);
} else {
myField.value += myValue;
}
}
export default {
props: {
@@ -11,6 +89,15 @@ export default {
required: true,
type: String
},
toolbar: {
type: Boolean,
default: false
},
showMarkdownHelp: {
// only used if toolbar is True - waiting on a general toolbar refactor
type: Function,
required: false
},
onupdate: {
type: Function
}
@@ -22,16 +109,95 @@ export default {
},
methods: {
update: _.debounce(function(e) {
this.input = e.target.value;
if (this.onupdate) {
this.onupdate(this.input);
}
}, 300)
}, 300),
insertMarkdown(markdown) {
const editorTextarea = this.$refs["editor"];
_insertAtCursor(editorTextarea, markdown);
Vue.nextTick(() => {
const event = new Event("input");
editorTextarea.dispatchEvent(event);
});
},
insertGalaxyMarkdownBlock(block) {
this.insertMarkdown(`${FENCE}galaxy\n${block}\n${FENCE}\n`);
},
_selectDataset(galaxyCall) {
dialog(
response => {
const datasetId = response.id;
this.insertGalaxyMarkdownBlock(`${galaxyCall}(history_dataset_id=${datasetId})`);
},
{
multiple: false,
format: null,
library: false // TODO: support?
}
);
},
selectDataset() {
this._selectDataset("history_dataset_display");
},
selectDatasetForImage() {
this._selectDataset("history_dataset_as_image");
},
selectDatasetCollection() {
datasetCollectionDialog(response => {
this.insertGalaxyMarkdownBlock(
`history_dataset_collection_display(history_dataset_collection_id=${response.id})`
);
}, {});
},
selectWorkflow() {
workflowDialog(response => {
this.insertGalaxyMarkdownBlock(`workflow_display(workflow_id=${response.id})`);
}, {});
}
}
};
</script>
<style scoped>
<style lang="scss" scoped>
.galaxymark-toolbar {
background: #fff;
border-bottom: 1px solid rgba(0, 0, 0, 0.1);
display: block;
width: 100%;
margin-top: 0;
margin-bottom: 0;
padding-left: 0;
padding-right: 0;
}
.galaxymark-toolbar li {
display: inline-block;
position: relative;
z-index: 1;
}
.galaxymark-toolbar li a {
color: #888;
cursor: pointer;
display: block;
font-size: 16px;
height: 40px;
line-height: 40px;
text-align: center;
transition: color 0.2s linear;
width: 40px;
}
.galaxymark-toolbar li a:hover {
color: #000;
text-decoration: none;
}
.markdown-text {
font: 16px/1.7 Menlo, Consolas, Monaco, "Andale Mono", monospace;
}
.markdown-textarea {
border: none;
border-right: 1px solid #ccc;
@@ -39,9 +205,9 @@ export default {
resize: none;
outline: none;
background-color: #f6f6f6;
font-size: 14px;
font-family: "Monaco", courier, monospace;
@extend .markdown-text;
padding: 20px;
width: 100%;
flex: 1;
}
</style>
client/galaxy/scripts/components/Markdown/help.js
+26
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@@ -0,0 +1,26 @@
export const markdownGeneralHelpHtml = `
<p>
For an overview of standard Markdown visit the
<a href="https://commonmark.org/help/tutorial/">commonmark.org tutorial</a>.
</p>
<p>
The Galaxy extensions to Markdown are represented as code blocks, these blocks start
with the line <tt>\`\`\`galaxy</tt> and end with the line <tt>\`\`\`</tt> and have a
command with arguments that reference parts of the workflow in the middle.
</p>`;
export const datasetCommandsHtml = `
<dt><tt>history_dataset_display</tt></dt>
<dd>Embed a dataset description in the resulting document.</dd>
<dt><tt>history_dataset_collection_display</tt></dt>
<dd>Embed a dataset collection description in the resulting document.</dd>
<dt><tt>history_dataset_as_image</tt></dt>
<dd>Embed a dataset as an image in the resulting document - the dataset should be an image datatype.</dd>
<dt><tt>history_dataset_peek</tt></dt>
<dd>Embed Galaxy's metadata attribute 'peek' into the resulting document - this is datatype dependent metadata but usually this is a few lines from the start of a file.</dd>
<dt><tt>history_dataset_info</tt></dt>
<dd>Embed Galaxy's metadata attribute 'info' into the resulting document - this is datatype dependent metadata but usually this is the program output that generated the dataset.</dd>
</dl>
</div>
`;
client/galaxy/scripts/components/PageDisplay/PageDisplay.vue
+43
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@@ -0,0 +1,43 @@
<template>
<markdown :markdown-config="markdownConfig"> </markdown>
</template>
<script>
import { getAppRoot } from "onload/loadConfig";
import axios from "axios";
import Markdown from "components/Markdown/Markdown.vue";
export default {
components: {
Markdown
},
props: {
pageId: {
type: String,
required: true
}
},
data() {
return {
markdownConfig: {}
};
},
created: function() {
const pageId = this.pageId;
const url = getAppRoot() + `api/pages/${pageId}`;
this.ajaxCall(url);
},
methods: {
ajaxCall: function(url) {
axios
.get(url)
.then(response => {
this.markdownConfig = { ...response.data, markdown: response.data.content };
})
.catch(e => {
console.error(e);
});
}
}
};
</script>
client/galaxy/scripts/components/PageDisplay/index.js
+4
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@@ -0,0 +1,4 @@
export { default as PageDisplay } from "./PageDisplay";
// function for mounting page display in non-Vue environments
export { mountPageDisplay } from "./mount";
client/galaxy/scripts/components/PageDisplay/mount.js
+15
View File
@@ -0,0 +1,15 @@
/**
* Endpoint for mounting PageDisplay from non-Vue environment (annotated DOMs).
*/
import $ from "jquery";
import Vue from "vue";
import PageDisplay from "./PageDisplay.vue";
export const mountPageDisplay = (propsData = {}) => {
$("#page-display-content").each((index, el) => {
const pageId = $(el).attr("page_id");
const component = Vue.extend(PageDisplay);
propsData.pageId = pageId;
return new component({ propsData: propsData }).$mount(el);
});
};
client/galaxy/scripts/components/PageEditor/PageEditor.vue
+42 -3
View File
@@ -3,15 +3,34 @@
<div class="unified-panel-header" unselectable="on">
<div class="unified-panel-header-inner">
Page Editor: {{ title }}
<a id="save-button" class="btn btn-secondary fa fa-save float-right" @click="saveContent"></a>
<a
id="save-button"
class="btn btn-secondary fa fa-save float-right"
href="javascript:void(0)"
@click="saveContent"
></a>
<a
id="view-button"
class="btn btn-secondary fa fa-eye float-right"
href="javascript:void(0)"
@click="viewContent"
></a>
</div>
</div>
<page-editor-html :page-id="pageId" :content="content" ref="contentEditor" />
<page-editor-html :page-id="pageId" :content="content" v-if="contentFormat == 'html'" ref="contentEditor" />
<page-editor-markdown
:page-id="pageId"
:initial-content="content"
v-if="contentFormat == 'markdown'"
ref="contentEditor"
/>
</span>
</template>
<script>
import { getAppRoot } from "onload/loadConfig";
import PageEditorHtml from "./PageEditorHtml";
import PageEditorMarkdown from "./PageEditorMarkdown";
export default {
props: {
@@ -19,20 +38,40 @@ export default {
required: true,
type: String
},
publicUrl: {
required: true,
type: String
},
content: {
type: String
},
contentFormat: {
type: String,
default: "html"
},
title: {
type: String
}
},
computed: {},
methods: {
saveContent: function() {
this.$refs.contentEditor.saveContent();
},
viewContent: function() {
// TODO: Future iteration, contentEditor should have an entry point that can decide
// if it has changed content.
const r = window.confirm(
"This will leave the current page editor, if you have unsaved changes they will be lost. Do you wish to continue?"
);
if (r === true) {
window.location = `${getAppRoot()}${this.publicUrl}`;
}
}
},
components: {
PageEditorHtml
PageEditorHtml,
PageEditorMarkdown
}
};
</script>
client/galaxy/scripts/components/PageEditor/PageEditorMarkdown.vue
+53
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@@ -0,0 +1,53 @@
<template>
<div class="unified-panel-body editor-body">
<markdown-editor
:initial-markdown="initialContent"
:onupdate="onUpdate"
ref="markdownEditor"
:toolbar="true"
:showMarkdownHelp="showMarkdownHelp"
>
</markdown-editor>
</div>
</template>
<script>
import MarkdownEditor from "components/Markdown/MarkdownEditor";
import { showMarkdownHelp } from "./markdownHelp";
import { save } from "./util";
export default {
components: {
MarkdownEditor
},
data: function() {
return {
content: "",
showMarkdownHelp: showMarkdownHelp
};
},
props: {
pageId: {
required: true,
type: String
},
initialContent: {
type: String
}
},
methods: {
onUpdate: function(content) {
this.content = content;
},
saveContent: function() {
save(this.pageId, this.content);
}
}
};
</script>
<style scoped>
.editor-body {
display: flex;
}
</style>
client/galaxy/scripts/components/PageEditor/markdownHelp.js
+87
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@@ -0,0 +1,87 @@
import { datasetCommandsHtml, markdownGeneralHelpHtml } from "components/Markdown/help";
const markdownHelp = `
<div>
<h3>Overview</h3>
<p>
This document Markdown document will be used to generate your Galaxy Page.
This document should be Markdown with embedded command for extracting and
displaying Galaxy objects and their metadata.
</p>
${markdownGeneralHelpHtml}
<h3>History Contents Commands</h3>
<p>
These commands reference a dataset. For instance, the following examples would display
the dataset collection corresponding to a Galaxy dataset collection ID and display a
single dataset as an image corresponding to a Galaxy dataset ID.
</p>
<pre>
\`\`\`galaxy
history_dataset_collection_display(history_dataset_collection_id=33b43b4e7093c91f)
\`\`\`
</pre>
<pre>
\`\`\`galaxy
history_dataset_as_image(history_dataset_id=33b43b4e7093c91f)
\`\`\`
</pre>
${datasetCommandsHtml}
<h3>Workflow Commands</h3>
<p>
These commands reference a workflow (currently only one). The following example would
display a representation of the workflow in the resulting Galaxy Page:
</p>
<pre>
\`\`\`galaxy
workflow_display(workflow_id=33b43b4e7093c91f>)
\`\`\`
</pre>
<dl>
<dt><tt>workflow_display</tt></dt>
<dd>Embed a description of the workflow itself in the resulting document.</dd>
</dl>
<h3>Job Commands</h3>
<p>
These commands reference a Galaxy job.For instance, the
following example would show the job parameters the job ID 33b43b4e7093c91f:
</p>
<pre>
\`\`\`galaxy
job_parameters(job_id=33b43b4e7093c91f)
\`\`\`
</pre>
<dt><tt>tool_stderr</tt></dt>
<dd>Embed the tool standard error stream for this job in the resulting document.</dd>
<dt><tt>tool_stdout</tt></dt>
<dd>Embed the tool standard output stream for this job in the resulting document.</dd>
<dt><tt>job_metrics</tt></dt>
<dd>Embed the job metrics for this job in the resulting document (if Galaxy is configured and you have permission).</dd>
<dt><tt>job_parameters</tt></dt>
<dd>Embed the tool parameters for this job in the resulting document.</dd>
`;
import $ from "jquery";
import { hide_modal, show_modal } from "layout/modal";
export function showMarkdownHelp() {
const markdownHelpBody = $(markdownHelp);
show_modal("Pages Markdown Help", markdownHelpBody, {
Ok: hide_modal
});
}
client/galaxy/scripts/components/PageEditor/util.js
+7 -16
View File
@@ -1,24 +1,15 @@
import $ from "jquery";
import axios from "axios";
import _l from "utils/localization";
import { getAppRoot } from "onload/loadConfig";
import { show_modal, hide_modal } from "layout/modal";
import { Toast } from "ui/toast";
import { errorMessageAsString } from "utils/simple-error";
export const save = (pageId, content) => {
console.log(`content is ${content}`);
show_modal(_l("Saving page"), _l("progress"));
// Do save.
$.ajax({
url: `${getAppRoot()}page/save`,
type: "POST",
data: {
id: pageId,
content: content,
_: "true"
},
success: function() {
hide_modal();
}
});
axios
.post(`${getAppRoot()}api/pages/${pageId}/revisions`, { content: content })
.finally(hide_modal)
.catch(error_message => Toast.error("Failed to save page: " + errorMessageAsString(error_message)));
};
client/galaxy/scripts/components/DataDialog/DataDialogSearch.vue → client/galaxy/scripts/components/SelectionDialog/DataDialogSearch.vue
View File
client/galaxy/scripts/components/DataDialog/DataDialogTable.vue → client/galaxy/scripts/components/SelectionDialog/DataDialogTable.vue
+5 -1
View File
@@ -12,7 +12,7 @@
@filtered="filtered"
>
<template v-slot:cell(label)="data">
<i v-if="data.item.isDataset" class="fa fa-file-o" /> <i v-else class="fa fa-folder" />
<i v-if="data.item.isLeaf" :class="leafIcon" /> <i v-else class="fa fa-folder" />
{{ data.value ? data.value : "-" }}
</template>
<template v-slot:cell(details)="data">
@@ -52,6 +52,10 @@ export default {
multiple: {
type: Boolean,
default: false
},
leafIcon: {
type: String,
default: "fa fa-file-o"
}
},
data() {
client/galaxy/scripts/components/SelectionDialog/DatasetCollectionDialog.test.js
+68
View File
@@ -0,0 +1,68 @@
import MockAdapter from "axios-mock-adapter";
import axios from "axios";
import DatasetCollectionDialog from "./DatasetCollectionDialog.vue";
import { __RewireAPI__ as rewire } from "./DatasetCollectionDialog";
import SelectionDialog from "./SelectionDialog.vue";
import { shallowMount, createLocalVue } from "@vue/test-utils";
const mockOptions = {
callback: () => {},
modalStatic: true,
history: "f2db41e1fa331b3e"
};
const galaxyInstance = {
root: "/"
};
describe("DatasetCollectionDialog.vue", () => {
let wrapper;
let localVue;
let axiosMock;
beforeEach(() => {
axiosMock = new MockAdapter(axios);
rewire.__Rewire__("getGalaxyInstance", () => galaxyInstance);
localVue = createLocalVue();
wrapper = shallowMount(DatasetCollectionDialog, {
propsData: mockOptions,
localVue: localVue
});
});
afterEach(() => {
axiosMock.restore();
});
it("loads correctly in loading state, shows options when optionsShow becomes true", async () => {
// Initially in loading state.
const collectionsResponse = [{ id: "f2db41e1fa331b3e", name: "Awesome Collection" }];
axiosMock
.onGet(`/api/histories/${mockOptions.history}/contents?type=dataset_collection`)
.reply(200, collectionsResponse);
expect(wrapper.find(SelectionDialog).is(SelectionDialog)).to.equals(true);
expect(wrapper.vm.optionsShow).to.equals(false);
await localVue.nextTick();
await localVue.nextTick();
await localVue.nextTick();
// why not shown?
expect(wrapper.vm.errorMessage).to.equals(null);
expect(wrapper.vm.optionsShow).to.equals(true);
});
it("error message set on dataset collection fetch problems", async () => {
expect(wrapper.vm.errorMessage).to.equals(null);
axiosMock
.onGet(`/api/histories/${mockOptions.history}/contents?type=dataset_collection`)
.reply(403, { err_msg: "Bad error" });
await localVue.nextTick();
await localVue.nextTick();
await localVue.nextTick();
await localVue.nextTick();
expect(wrapper.vm.errorMessage).to.equals("Bad error");
});
});
client/galaxy/scripts/components/SelectionDialog/DatasetCollectionDialog.vue
+84
View File
@@ -0,0 +1,84 @@
<template>
<selection-dialog
:errorMessage="errorMessage"
:optionsShow="optionsShow"
:modalShow="modalShow"
:hideModal="() => (modalShow = false)"
>
<template v-slot:search>
<data-dialog-search v-model="filter" />
</template>
<template v-slot:options>
<data-dialog-table
v-if="optionsShow"
:items="items"
:multiple="false"
:filter="filter"
leafIcon="fa fa-folder"
@clicked="clicked"
@load="load"
/>
</template>
</selection-dialog>
</template>
<script>
import axios from "axios";
import SelectionDialogMixin from "./SelectionDialogMixin";
import { getGalaxyInstance } from "app";
import { errorMessageAsString } from "utils/simple-error";
export default {
mixins: [SelectionDialogMixin],
props: {
history: {
type: String,
required: true
}
},
data() {
return {
errorMessage: null,
filter: null,
items: [],
modalShow: true,
optionsShow: false,
hasValue: false
};
},
created: function() {
this.load();
},
methods: {
formatRows() {},
clicked: function(record) {
this.modalShow = false;
this.callback(record);
},
/** Performs server request to retrieve data records **/
load: function() {
this.filter = null;
this.optionsShow = false;
const Galaxy = getGalaxyInstance();
const url = `${Galaxy.root}api/histories/${this.history}/contents?type=dataset_collection`;
axios
.get(url)
.then(response => {
this.items = response.data.map(item => {
return {
id: item.id,
label: item.name,
time: item.created_time,
isLeaf: true
};
});
this.formatRows();
this.optionsShow = true;
})
.catch(errorMessage => {
this.errorMessage = errorMessageAsString(errorMessage);
});
}
}
};
</script>
client/galaxy/scripts/components/SelectionDialog/SelectionDialog.test.js
+53
View File
@@ -0,0 +1,53 @@
import SelectionDialog from "./SelectionDialog.vue";
import { mount, createLocalVue } from "@vue/test-utils";
const mockOptions = {
callback: () => {},
modalStatic: true
};
describe("SelectionDialog.vue", () => {
let wrapper;
let localVue;
let calledHide = false;
beforeEach(() => {
localVue = createLocalVue();
mockOptions.hideModal = () => {
calledHide = true;
};
wrapper = mount(SelectionDialog, {
slots: {
options: "<tree-options />",
search: "<cool-search />"
},
propsData: mockOptions,
localVue
});
});
it("loads correctly in loading state, shows options when optionsShow becomes true", async () => {
expect(wrapper.find(".fa-spinner").text()).to.equals("");
expect(wrapper.contains(".fa-spinner")).to.equals(true);
expect(wrapper.contains("tree-options")).to.equals(false);
wrapper.setProps({ optionsShow: true });
await localVue.nextTick();
expect(wrapper.contains(".fa-spinner")).to.equals(false);
expect(wrapper.contains("tree-options")).to.equals(true);
});
it("loads search correctly", async () => {
await localVue.nextTick();
expect(wrapper.contains("cool-search")).to.equals(true);
});
it("hideModal called on click cancel", async () => {
expect(calledHide).to.equals(false);
expect(wrapper.contains(".selection-dialog-modal-cancel")).to.equals(true);
wrapper.setProps({ optionsShow: true });
await localVue.nextTick();
wrapper.find(".selection-dialog-modal-cancel").trigger("click");
await localVue.nextTick();
expect(calledHide).to.equals(true);
});
});
client/galaxy/scripts/components/SelectionDialog/SelectionDialog.vue
+69
View File
@@ -0,0 +1,69 @@
<template>
<b-modal
modal-class="selection-dialog-modal"
v-if="modalShow"
visible
ok-only
ok-title="Close"
:static="modalStatic"
>
<template v-slot:modal-header>
<slot name="search"> </slot>
</template>
<b-alert v-if="errorMessage" variant="danger" show v-html="errorMessage" />
<div v-else>
<slot name="options" v-if="optionsShow"> </slot>
<div v-else><span class="fa fa-spinner fa-spin" /> <span>Please wait...</span></div>
</div>
<template v-if="!errorMessage" v-slot:modal-footer>
<div class="w-100">
<slot name="buttons"> </slot>
<b-btn size="sm" class="float-right selection-dialog-modal-cancel" @click="hideModal"> Cancel </b-btn>
</div>
</template>
</b-modal>
</template>
<script>
import Vue from "vue";
import BootstrapVue from "bootstrap-vue";
Vue.use(BootstrapVue);
export default {
props: {
multiple: {
type: Boolean,
default: false
},
modalStatic: {
type: Boolean,
default: false
},
errorMessage: {
type: String,
default: null
},
optionsShow: {
type: Boolean,
default: false
},
modalShow: {
type: Boolean,
default: true
},
hideModal: {
type: Function,
required: true
}
}
};
</script>
<style>
.selection-dialog-modal .modal-body {
max-height: 50vh;
height: 50vh;
overflow-y: auto;
}
</style>
client/galaxy/scripts/components/SelectionDialog/SelectionDialogMixin.js
+17
View File
@@ -0,0 +1,17 @@
import DataDialogSearch from "./DataDialogSearch.vue";
import DataDialogTable from "./DataDialogTable.vue";
import SelectionDialog from "./SelectionDialog.vue";
export default {
components: {
"selection-dialog": SelectionDialog,
"data-dialog-table": DataDialogTable,
"data-dialog-search": DataDialogSearch
},
props: {
callback: {
type: Function,
required: true
}
}
};
client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.test.js
+69
View File
@@ -0,0 +1,69 @@
import MockAdapter from "axios-mock-adapter";
import axios from "axios";
import WorkflowDialog from "./WorkflowDialog.vue";
import { __RewireAPI__ as rewire } from "components/Workflow/services";
import SelectionDialog from "./SelectionDialog.vue";
import { shallowMount, createLocalVue } from "@vue/test-utils";
const mockOptions = {
callback: () => {},
modalStatic: true
};
const userModel = {
get: () => "username"
};
const galaxyInstance = {
root: "/",
user: userModel
};
describe("WorkflowDialog.vue", () => {
let wrapper;
let localVue;
let axiosMock;
beforeEach(() => {
axiosMock = new MockAdapter(axios);
rewire.__Rewire__("getGalaxyInstance", () => galaxyInstance);
rewire.__Rewire__("_addAttributes", workflow => workflow);
localVue = createLocalVue();
wrapper = shallowMount(WorkflowDialog, {
propsData: mockOptions,
localVue: localVue
});
});
afterEach(() => {
axiosMock.restore();
});
it("loads correctly in loading state, shows options when optionsShow becomes true", async () => {
// Initially in loading state.
const workflowsResponse = [{ id: "f2db41e1fa331b3e", name: "Awesome Workflow" }];
axiosMock.onGet("/api/workflows").reply(200, workflowsResponse);
expect(wrapper.find(SelectionDialog).is(SelectionDialog)).to.equals(true);
expect(wrapper.vm.optionsShow).to.equals(false);
await localVue.nextTick();
await localVue.nextTick();
await localVue.nextTick();
// why not shown?
expect(wrapper.vm.errorMessage).to.equals(null);
expect(wrapper.vm.optionsShow).to.equals(true);
});
it("error message set on workflow fetch problems", async () => {
expect(wrapper.vm.errorMessage).to.equals(null);
axiosMock.onGet("/api/workflows").reply(403, { err_msg: "Bad error" });
await localVue.nextTick();
await localVue.nextTick();
await localVue.nextTick();
await localVue.nextTick();
expect(wrapper.vm.errorMessage).to.equals("Bad error");
});
});
client/galaxy/scripts/components/SelectionDialog/WorkflowDialog.vue
+76
View File
@@ -0,0 +1,76 @@
<template>
<selection-dialog
:errorMessage="errorMessage"
:optionsShow="optionsShow"
:modalShow="modalShow"
:hideModal="() => (modalShow = false)"
>
<template v-slot:search>
<data-dialog-search v-model="filter" />
</template>
<template v-slot:options>
<data-dialog-table
v-if="optionsShow"
:items="items"
:multiple="false"
:filter="filter"
leafIcon="fa fa-sitemap fa-rotate-270"
@clicked="clicked"
@load="load"
/>
</template>
</selection-dialog>
</template>
<script>
import SelectionDialogMixin from "./SelectionDialogMixin";
import { Services } from "components/Workflow/services";
export default {
mixins: [SelectionDialogMixin],
props: {},
data() {
return {
errorMessage: null,
filter: null,
items: [],
modalShow: true,
optionsShow: false,
hasValue: false
};
},
created: function() {
this.services = new Services();
this.load();
},
methods: {
formatRows() {},
clicked: function(record) {
this.modalShow = false;
this.callback(record);
},
/** Performs server request to retrieve data records **/
load: function() {
this.filter = null;
this.optionsShow = false;
this.services
.getWorkflows()
.then(items => {
this.items = items.map(item => {
return {
id: item.id,
label: item.name,
time: item.create_time,
isLeaf: true
};
});
this.formatRows();
this.optionsShow = true;
})
.catch(errorMessage => {
this.errorMessage = errorMessage.toString();
});
}
}
};
</script>
client/galaxy/scripts/components/Workflow/Editor/WorkflowEditor.vue
+1 -1
View File
@@ -100,7 +100,7 @@
</div>
</div>
<div class="unified-panel-body workflow-report-body" v-show="mode == 'report'">
<markdown-editor ref="report-editor" initial-markdown="" :onupdate="onReportUpdate" />
<markdown-editor ref="report-editor" initial-markdown="" :onupdate="onReportUpdate" :toolbar="false" />
</div>
</div>
</template>
client/galaxy/scripts/components/Workflow/Editor/reportHelp.js
+5 -20
View File
@@ -1,3 +1,5 @@
import { datasetCommandsHtml, markdownGeneralHelpHtml } from "components/Markdown/help";
const reportHelp = `
<div>
<h3>Overview</h3>
@@ -6,16 +8,10 @@ const reportHelp = `
This document Markdown document will be used to generate a report
for invocations of this workflow. This document should be Markdown
with embedded command for extracting and displaying parts of the workflow,
its invocation metadata, its inputs and outputs, etc.. For an overview
of standard Markdown visit the <a href="https://commonmark.org/help/tutorial/">commonmark.org
tutorial</a>.
its invocation metadata, its inputs and outputs, etc..
</p>
<p>
The Galaxy extensions to Markdown are represented as code blocks, these blocks start
with the line <tt>\`\`\`galaxy</tt> and end with the line <tt>\`\`\`</tt> and have a
command with arguments that reference parts of the workflow in the middle.
</p>
${markdownGeneralHelpHtml}
<h3>Workflow Commands</h3>
@@ -78,18 +74,7 @@ history_dataset_collection_display(output="Merged Bam")
\`\`\`
</pre>
<dt><tt>history_dataset_display</tt></dt>
<dd>Embed a dataset description in the resulting report.</dd>
<dt><tt>history_dataset_collection_display</tt></dt>
<dd>Embed a dataset collection description in the resulting report.</dd>
<dt><tt>history_dataset_as_image</tt></dt>
<dd>Embed a dataset as an image in the resulting report - the dataset should be an image datatype.</dd>
<dt><tt>history_dataset_peek</tt></dt>
<dd>Embed Galaxy's metadata attribute 'peek' into the resulting report - this is datatype dependent metadata but usually this is a few lines from the start of a file.</dd>
<dt><tt>history_dataset_info</tt></dt>
<dd>Embed Galaxy's metadata attribute 'info' into the resulting report - this is datatype dependent metadata but usually this is the program output that generated the dataset.</dd>
</dl>
</div>
${datasetCommandsHtml}
`;
import $ from "jquery";
client/galaxy/scripts/components/Workflow/services.js
+1 -1
View File
@@ -5,7 +5,7 @@ import { rethrowSimple } from "utils/simple-error";
/** Workflow data request helper **/
export class Services {
constructor(options = {}) {
this.root = options.root;
this.root = options.root || getGalaxyInstance().root;
}
async copyWorkflow(workflow) {
client/galaxy/scripts/galaxy.pages.js
+5 -2
View File
@@ -10,12 +10,15 @@ export default function pagesEditorOnload() {
axios
.get(`${getAppRoot()}api/pages/${pageId}`)
.then(response => {
const data = response.data;
const pageEditorInstance = Vue.extend(PageEditor);
new pageEditorInstance({
propsData: {
publicUrl: `u/${data.username}/p/${data.slug}`,
pageId: pageId,
content: response.data.content,
title: response.data.title
content: data.content,
contentFormat: data.content_format,
title: data.title
},
el: "#page-editor-content"
});
client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
-16
View File
@@ -1,7 +1,6 @@
import jQuery from "jquery";
import _ from "underscore";
import Backbone from "backbone";
import { getGalaxyInstance } from "app";
import BASE_MVC from "mvc/base-mvc";
//=============================================================================
@@ -28,15 +27,11 @@ var ControlledFetchCollection = Backbone.Collection.extend({
*/
fetch: function(options) {
options = this._buildFetchOptions(options);
const Galaxy = getGalaxyInstance();
Galaxy.debug("fetch options:", options);
return Backbone.Collection.prototype.fetch.call(this, options);
},
/** build ajax data/parameters from options */
_buildFetchOptions: function(options) {
const Galaxy = getGalaxyInstance();
// note: we normally want options passed in to override the defaults built here
// so most of these fns will generate defaults
options = _.clone(options) || {};
@@ -52,15 +47,12 @@ var ControlledFetchCollection = Backbone.Collection.extend({
// (i.e. this.on( 'sync', function( options ){ if( options.limit ){ ... } }))
// however, when we send to xhr/jquery we copy them to data also so that they become API query params
options.data = options.data || this._buildFetchData(options);
Galaxy.debug("data:", options.data);
// options.data.filters --> options.data.q, options.data.qv
var filters = this._buildFetchFilters(options);
Galaxy.debug("filters:", filters);
if (!_.isEmpty(filters)) {
_.extend(options.data, this._fetchFiltersToAjaxData(filters));
}
Galaxy.debug("data:", options.data);
return options;
},
@@ -271,8 +263,6 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
/** fetch the first 'page' of data */
fetchFirst: function(options) {
const Galaxy = getGalaxyInstance();
Galaxy.debug("ControlledFetchCollection.fetchFirst:", options);
options = options ? _.clone(options) : {};
this.allFetched = false;
this.lastFetched = 0;
@@ -286,13 +276,9 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
/** fetch the next page of data */
fetchMore: function(options) {
const Galaxy = getGalaxyInstance();
Galaxy.debug("ControlledFetchCollection.fetchMore:", options);
options = _.clone(options || {});
var collection = this;
Galaxy.debug("fetchMore, options.reset:", options.reset);
if (!options.reset && collection.allFetched) {
return jQuery.when();
}
@@ -305,7 +291,6 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
options.offset = collection.lastFetched;
}
var limit = (options.limit = options.limit || collection.limitPerFetch || null);
Galaxy.debug("fetchMore, limit:", limit, "offset:", options.offset);
collection.trigger("fetching-more");
return (
@@ -318,7 +303,6 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
.done(function _postFetchMore(fetchedData) {
var numFetched = _.isArray(fetchedData) ? fetchedData.length : 0;
collection.lastFetched += numFetched;
Galaxy.debug("fetchMore, lastFetched:", collection.lastFetched);
// anything less than a full page means we got all there is to get
if (!limit || numFetched < limit) {
collection.allFetched = true;
client/galaxy/scripts/utils/data.js
+37 -6
View File
@@ -2,6 +2,8 @@ import $ from "jquery";
import axios from "axios";
import Vue from "vue";
import DataDialog from "components/DataDialog/DataDialog.vue";
import WorkflowDialog from "components/SelectionDialog/WorkflowDialog.vue";
import DatasetCollectionDialog from "components/SelectionDialog/DatasetCollectionDialog.vue";
import { getGalaxyInstance } from "app";
import { getAppRoot } from "onload/loadConfig";
@@ -41,15 +43,44 @@ export function dialog(callback, options = {}) {
root: galaxy.root,
host: host
});
const instance = Vue.extend(DataDialog);
const vm = document.createElement("div");
$("body").append(vm);
new instance({
propsData: options
}).$mount(vm);
_mountSelectionDialog(DataDialog, options);
});
}
/**
* Opens a modal dialog for workflow selection
* @param {function} callback - Result function called with selection
*/
export function workflowDialog(callback, options = {}) {
Object.assign(options, {
callback: callback
});
_mountSelectionDialog(WorkflowDialog, options);
}
/**
* Opens a modal dialog for dataset collection selection
* @param {function} callback - Result function called with selection
*/
export function datasetCollectionDialog(callback, options = {}) {
getCurrentGalaxyHistory().then(history_id => {
Object.assign(options, {
callback: callback,
history: history_id
});
_mountSelectionDialog(DatasetCollectionDialog, options);
});
}
function _mountSelectionDialog(clazz, options) {
const instance = Vue.extend(clazz);
const vm = document.createElement("div");
$("body").append(vm);
new instance({
propsData: options
}).$mount(vm);
}
/**
* Creates a history dataset by submitting an upload request
* TODO: This should live somewhere else.
client/galaxy/scripts/utils/simple-error.js
+6 -2
View File
@@ -1,9 +1,13 @@
export function rethrowSimple(e) {
export function errorMessageAsString(e) {
let message = "Request failed.";
if (e.response) {
message = e.response.data.err_msg || `${e.response.statusText} (${e.response.status})`;
} else if (typeof e == "string") {
message = e;
}
throw message;
return message;
}
export function rethrowSimple(e) {
throw errorMessageAsString(e);
}
lib/galaxy/managers/markdown_util.py
+35 -10
View File
@@ -13,6 +13,7 @@ context specific processing.
import logging
import re
from galaxy.exceptions import MalformedContents, MalformedId
from galaxy.managers.collections import DatasetCollectionManager
from galaxy.managers.hdas import HDAManager
from galaxy.managers.hdcas import HDCASerializer
@@ -53,7 +54,8 @@ OUTPUT_LABEL_PATTERN = re.compile(r'output=\s*%s\s*' % ARG_VAL_CAPTURED_REGEX)
INPUT_LABEL_PATTERN = re.compile(r'input=\s*%s\s*' % ARG_VAL_CAPTURED_REGEX)
STEP_LABEL_PATTERN = re.compile(r'step=\s*%s\s*' % ARG_VAL_CAPTURED_REGEX)
# STEP_OUTPUT_LABEL_PATTERN = re.compile(r'step_output=([\w_\-]+)/([\w_\-]+)')
ID_PATTERN = re.compile(r'(workflow_id|history_dataset_id|history_dataset_collection_id|job_id)=([\d]+)')
UNENCODED_ID_PATTERN = re.compile(r'(workflow_id|history_dataset_id|history_dataset_collection_id|job_id)=([\d]+)')
ENCODED_ID_PATTERN = re.compile(r'(workflow_id|history_dataset_id|history_dataset_collection_id|job_id)=([a-z0-9]+)')
GALAXY_FLAVORED_MARKDOWN_CONTAINER_LINE_PATTERN = re.compile(
r"```\s*galaxy\s*"
)
@@ -66,6 +68,27 @@ VALID_CONTAINER_END_PATTERN = re.compile(r"^```\s*$")
WHITE_SPACE_ONLY_PATTERN = re.compile(r"^[\s]+$")
def ready_galaxy_markdown_for_import(trans, external_galaxy_markdown):
"""Convert from encoded IDs to decoded numeric IDs for storing in the DB."""
validate_galaxy_markdown(external_galaxy_markdown, internal=False)
def _remap(container, line):
id_match = re.search(ENCODED_ID_PATTERN, line)
object_id = None
if id_match:
object_id = id_match.group(2)
try:
decoded_id = trans.security.decode_id(object_id)
except Exception:
raise MalformedId("Invalid encoded ID %s" % object_id)
line = line.replace(id_match.group(), "%s=%d" % (id_match.group(1), decoded_id))
return (line, False)
internal_markdown = _remap_galaxy_markdown_calls(_remap, external_galaxy_markdown)
return internal_markdown
def ready_galaxy_markdown_for_export(trans, internal_galaxy_markdown):
"""Fill in details needed to render Galaxy flavored markdown.
@@ -76,10 +99,13 @@ def ready_galaxy_markdown_for_export(trans, internal_galaxy_markdown):
"""
hdas_manager = HDAManager(trans.app)
workflows_manager = WorkflowsManager(trans.app)
job_manager = JobManager(trans.app)
collection_manager = DatasetCollectionManager(trans.app)
extra_rendering_data = {}
def _remap(container, line):
id_match = re.search(ID_PATTERN, line)
id_match = re.search(UNENCODED_ID_PATTERN, line)
object_id = None
encoded_id = None
if id_match:
@@ -112,13 +138,12 @@ def ready_galaxy_markdown_for_export(trans, internal_galaxy_markdown):
elif container == "history_dataset_info":
hda = hdas_manager.get_accessible(object_id, trans.user)
info = hda.info
extend_history_dataset_rendering_data("info", info, "*No Dataset Peek Available*")
extend_history_dataset_rendering_data("info", info, "*No Dataset Info Available*")
elif container == "workflow_display":
# TODO: should be workflow id...
stored_workflow = workflows_manager.get_stored_accessible_workflow(trans, encoded_id)
ensure_rendering_data_for("workflows", encoded_id)["name"] = stored_workflow.name
elif container == "history_dataset_collection_display":
collection_manager = DatasetCollectionManager(trans.app)
hdca = collection_manager.get_dataset_collection_instance(trans, "history", encoded_id)
hdca_serializer = HDCASerializer(trans.app)
hdca_view = hdca_serializer.serialize_to_view(
@@ -128,11 +153,9 @@ def ready_galaxy_markdown_for_export(trans, internal_galaxy_markdown):
extra_rendering_data["history_dataset_collections"] = {}
ensure_rendering_data_for("history_dataset_collections", encoded_id).update(hdca_view)
elif container == "tool_stdout":
job_manager = JobManager(trans.app)
job = job_manager.get_accessible_job(trans, object_id)
ensure_rendering_data_for("jobs", encoded_id)["tool_stdout"] = job.tool_stdout or "*No Standard Output Available*"
elif container == "tool_stderr":
job_manager = JobManager(trans.app)
job = job_manager.get_accessible_job(trans, object_id)
ensure_rendering_data_for("jobs", encoded_id)["tool_stderr"] = job.tool_stderr or "*No Standard Error Available*"
return (line, False)
@@ -238,13 +261,11 @@ history_dataset_collection_display(input=%s)
line = line.replace(target_match.group(), "%s_id=%s" % (ref_object_type, ref_object.id))
return (line, False)
log.debug("workflow markdown is \n%s" % workflow_markdown)
workflow_markdown = _remap_galaxy_markdown_calls(
_section_remap,
workflow_markdown,
)
galaxy_markdown = _remap_galaxy_markdown_calls(_remap, workflow_markdown)
log.debug("galaxy markdown is \n%s" % galaxy_markdown)
return galaxy_markdown
@@ -258,7 +279,7 @@ def validate_galaxy_markdown(galaxy_markdown, internal=True):
def invalid_line(template, **kwd):
if "line" in kwd:
kwd["line"] = line.rstrip("\r\n")
raise Exception("Invalid line %d: %s" % (line_no + 1, template.format(**kwd)))
raise MalformedContents("Invalid line %d: %s" % (line_no + 1, template.format(**kwd)))
expecting_container_close = expecting_container_close_for is not None
if not fenced and expecting_container_close:
@@ -267,13 +288,16 @@ def validate_galaxy_markdown(galaxy_markdown, internal=True):
elif not fenced:
continue
elif fenced and expecting_container_close and BLOCK_FENCE_END.match(line):
# reset
expecting_container_close_for = None
function_calls = 0
elif open_fence and GALAXY_FLAVORED_MARKDOWN_CONTAINER_LINE_PATTERN.match(line):
if expecting_container_close:
if not VALID_CONTAINER_END_PATTERN.match(line):
invalid_line("Invalid command close line [{line}] for [{expected_for}]", line=line, expected_for=expecting_container_close_for)
# else closing container and we're done
expecting_container_close_for = None
function_calls = 0
continue
expecting_container_close_for = line
@@ -291,7 +315,7 @@ def validate_galaxy_markdown(galaxy_markdown, internal=True):
continue
if expecting_container_close_for:
raise Exception("Invalid line %d: %s" % (last_line_no, "close of block for [{expected_for}] expected".format(expected_for=expecting_container_close_for)))
raise MalformedContents("Invalid line %d: %s" % (last_line_no, "close of block for [{expected_for}] expected".format(expected_for=expecting_container_close_for)))
def _remap_galaxy_markdown_containers(func, markdown):
@@ -360,5 +384,6 @@ def _split_markdown_lines(markdown):
__all__ = (
'ready_galaxy_markdown_for_export',
'ready_galaxy_markdown_for_import',
'resolve_invocation_markdown',
)
lib/galaxy/managers/pages.py
+43 -17
View File
@@ -14,6 +14,10 @@ from six.moves.html_parser import HTMLParser
from galaxy import exceptions, model
from galaxy.managers import base, sharable
from galaxy.managers.hdas import HDAManager
from galaxy.managers.markdown_util import (
ready_galaxy_markdown_for_export,
ready_galaxy_markdown_for_import,
)
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.util import unicodify
from galaxy.util.sanitize_html import sanitize_html
@@ -87,7 +91,8 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
raise exceptions.DuplicatedSlugException("Page identifier must be unique")
content = payload.get("content", "")
content = self.rewrite_content_for_import(trans, content)
content_format = payload.get("content_format", "html")
content = self.rewrite_content_for_import(trans, content, content_format)
# Create the new stored page
page = trans.app.model.Page()
@@ -105,6 +110,7 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
page_revision.page = page
page.latest_revision = page_revision
page_revision.content = content
page_revision.content_format = content_format
# Persist
session = trans.sa_session
session.add(page)
@@ -114,46 +120,66 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
def save_new_revision(self, trans, page, payload):
# Assumes security has already been checked by caller.
content = payload.get("content", None)
content_format = payload.get("content_format", None)
if not content:
raise exceptions.ObjectAttributeMissingException("content undefined or empty")
if content_format not in [None, "html", "markdown"]:
raise exceptions.RequestParameterInvalidException("content_format [%s], if specified, must be either html or markdown" % content_format)
if 'title' in payload:
title = payload['title']
else:
title = page.title
content = self.rewrite_content_for_import(trans, content)
if content_format is None:
content_format = page.latest_revision.content_format
content = self.rewrite_content_for_import(trans, content, content_format=content_format)
page_revision = trans.app.model.PageRevision()
page_revision.title = title
page_revision.page = page
page.latest_revision = page_revision
page_revision.content = content
page_revision.content_format = content_format
# Persist
session = trans.sa_session
session.flush()
return page_revision
def rewrite_content_for_import(self, trans, content):
try:
content = sanitize_html(content)
processor = PageContentProcessor(trans, placeholderRenderForSave)
processor.feed(content)
# Output is string, so convert to unicode for saving.
content = unicodify(processor.output(), 'utf-8')
except exceptions.MessageException:
raise
except Exception:
raise exceptions.RequestParameterInvalidException("problem with embedded HTML content [%s]" % content)
def rewrite_content_for_import(self, trans, content, content_format):
if content_format == "html":
try:
content = sanitize_html(content)
processor = PageContentProcessor(trans, placeholderRenderForSave)
processor.feed(content)
# Output is string, so convert to unicode for saving.
content = unicodify(processor.output(), 'utf-8')
except exceptions.MessageException:
raise
except Exception:
raise exceptions.RequestParameterInvalidException("problem with embedded HTML content [%s]" % content)
elif content_format == "markdown":
content = ready_galaxy_markdown_for_import(trans, content)
else:
raise exceptions.RequestParameterInvalidException("content_format [%s] must be either html or markdown" % content_format)
return content
def rewrite_content_for_export(self, trans, as_dict):
content = as_dict["content"]
processor = PageContentProcessor(trans, placeholderRenderForEdit)
processor.feed(content)
content = unicodify(processor.output(), 'utf-8')
as_dict["content"] = content
content_format = as_dict.get("content_format", "html")
if content_format == "html":
processor = PageContentProcessor(trans, placeholderRenderForEdit)
processor.feed(content)
content = unicodify(processor.output(), 'utf-8')
as_dict["content"] = content
elif content_format == "markdown":
content, extra_attributes = ready_galaxy_markdown_for_export(trans, content)
as_dict["content"] = content
as_dict.update(extra_attributes)
else:
raise exceptions.RequestParameterInvalidException("content_format [%s] must be either html or markdown" % content_format)
return as_dict
lib/galaxy/model/__init__.py
+9 -2
View File
@@ -5767,7 +5767,8 @@ class CloudAuthz(RepresentById):
class Page(Dictifiable, RepresentById):
dict_element_visible_keys = ['id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted']
# username needed for slug generation
dict_element_visible_keys = ['id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted', 'username']
def __init__(self):
self.id = None
@@ -5787,14 +5788,20 @@ class Page(Dictifiable, RepresentById):
rval['revision_ids'] = rev
return rval
@property
def username(self):
return self.user.username
class PageRevision(Dictifiable, RepresentById):
dict_element_visible_keys = ['id', 'page_id', 'title', 'content']
DEFAULT_CONTENT_FORMAT = 'html'
dict_element_visible_keys = ['id', 'page_id', 'title', 'content', 'content_format']
def __init__(self):
self.user = None
self.title = None
self.content = None
self.content_format = PageRevision.DEFAULT_CONTENT_FORMAT
def to_dict(self, view='element'):
rval = super(PageRevision, self).to_dict(view=view)
lib/galaxy/model/mapping.py
+2 -1
View File
@@ -1246,7 +1246,8 @@ model.PageRevision.table = Table(
Column("update_time", DateTime, default=now, onupdate=now),
Column("page_id", Integer, ForeignKey("page.id"), index=True, nullable=False),
Column("title", TEXT),
Column("content", TEXT))
Column("content", TEXT),
Column("content_format", TrimmedString(32)))
model.PageUserShareAssociation.table = Table(
"page_user_share_association", metadata,
lib/galaxy/model/migrate/versions/0164_page_format.py
+30
View File
@@ -0,0 +1,30 @@
"""
Adds page content format.
"""
import datetime
import logging
from sqlalchemy import Column, MetaData
from galaxy.model.custom_types import TrimmedString
from galaxy.model.migrate.versions.util import add_column, drop_column
now = datetime.datetime.utcnow
log = logging.getLogger(__name__)
metadata = MetaData()
def upgrade(migrate_engine):
metadata.bind = migrate_engine
print(__doc__)
metadata.reflect()
content_format_column = Column('content_format', TrimmedString(32), default='html', server_default="html", nullable=False)
add_column(content_format_column, 'page_revision', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('content_format', 'page_revision', metadata)
lib/galaxy/webapps/galaxy/api/page_revisions.py
+1 -2
View File
@@ -52,8 +52,7 @@ class PageRevisionsController(BaseAPIController, SharableItemSecurityMixin, Uses
:param page_id: Add revision to Page with ID=page_id
:param payload: A dictionary containing::
'title' = New title of the page
'content' = New content of the page
'content' = New content of new page revision
:rtype: dictionary
:returns: Dictionary with 'success' or 'error' element to indicate the result of the request
lib/galaxy/webapps/galaxy/api/pages.py
+6 -4
View File
@@ -72,10 +72,11 @@ class PagesController(BaseAPIController, SharableItemSecurityMixin, UsesAnnotati
Create a page and return dictionary containing Page summary
:param payload: dictionary structure containing::
'slug' = The title slug for the page URL, must be unique
'title' = Title of the page
'content' = HTML contents of the page
'annotation' = Annotation that will be attached to the page
'slug' = The title slug for the page URL, must be unique
'title' = Title of the page
'content' = contents of the first page revision (type dependent on content_format)
'content_format' = 'html' or 'markdown'
'annotation' = Annotation that will be attached to the page
:rtype: dict
:returns: Dictionary return of the Page.to_dict call
@@ -120,5 +121,6 @@ class PagesController(BaseAPIController, SharableItemSecurityMixin, UsesAnnotati
page = get_object(trans, id, 'Page', check_ownership=False, check_accessible=True)
rval = self.encode_all_ids(trans, page.to_dict(), True)
rval['content'] = page.latest_revision.content
rval['content_format'] = page.latest_revision.content_format
self.manager.rewrite_content_for_export(trans, rval)
return rval
lib/galaxy/webapps/galaxy/controllers/page.py
+18 -14
View File
@@ -333,6 +333,12 @@ class PageController(BaseUIController, SharableMixin,
'name' : 'annotation',
'label' : 'Annotation',
'help' : 'A description of the page. The annotation is shown alongside published pages.'
}, {
'name' : 'content_format',
'label' : 'Content Format',
'type' : 'select',
'options' : [('HTML', 'html'), ('Markdown', 'markdown')],
'help' : 'Use the traditional rich HTML editor or the newer experimental Markdown editor to create the page content. The HTML editor has several known bugs, is unmaintained and pages created with it will be read-only in future releases of Galaxy.'
}]
}
else:
@@ -448,14 +454,6 @@ class PageController(BaseUIController, SharableMixin,
email=email,
use_panels=use_panels)
@web.expose
@web.require_login()
def save(self, trans, id, content):
id = self.decode_id(id)
page = trans.sa_session.query(model.Page).get(id)
assert page.user == trans.user
self.page_manager.save_new_revision(trans, page, {"content": content})
@web.expose
@web.require_login()
def display(self, trans, id):
@@ -478,11 +476,17 @@ class PageController(BaseUIController, SharableMixin,
# Security check raises error if user cannot access page.
self.security_check(trans, page, False, True)
# Process page content.
processor = PageContentProcessor(trans, self._get_embed_html)
processor.feed(page.latest_revision.content)
# Output is string, so convert to unicode for display.
page_content = unicodify(processor.output(), 'utf-8')
latest_revision = page.latest_revision
if latest_revision.content_format == "html":
# Process page content.
processor = PageContentProcessor(trans, self._get_embed_html)
processor.feed(page.latest_revision.content)
# Output is string, so convert to unicode for display.
page_content = unicodify(processor.output(), 'utf-8')
template = "page/display.mako"
else:
page_content = trans.security.encode_id(page.id)
template = "page/display_markdown.mako"
# Get rating data.
user_item_rating = 0
@@ -494,7 +498,7 @@ class PageController(BaseUIController, SharableMixin,
user_item_rating = 0
ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, page)
return trans.fill_template_mako("page/display.mako", item=page,
return trans.fill_template_mako(template, item=page,
item_data=page_content,
user_item_rating=user_item_rating,
ave_item_rating=ave_item_rating,
lib/galaxy_test/api/test_pages.py
+31 -3
View File
@@ -22,10 +22,16 @@ class BasePageApiTestCase(ApiTestCase):
return page_response.json()
def _test_page_payload(self, **kwds):
content_format = kwds.get("content_format", "html")
if content_format == "html":
content = "<p>Page!</p>"
else:
content = "*Page*\n\n"
request = dict(
slug="mypage",
title="MY PAGE",
content="<p>Page!</p>",
content=content,
content_format=content_format,
)
request.update(**kwds)
return request
@@ -41,7 +47,7 @@ class PageApiTestCase(BasePageApiTestCase):
create_response_json = self._create_valid_page_with_slug("indexpage")
assert self._users_index_has_page_with_id(create_response_json["id"])
def test_index_doesnt_show_unavailable_pages(self):
def test_index_does_not_show_unavailable_pages(self):
create_response_json = self._create_valid_page_as("others_page_index@bx.psu.edu", "otherspageindex")
assert not self._users_index_has_page_with_id(create_response_json["id"])
@@ -53,6 +59,13 @@ class PageApiTestCase(BasePageApiTestCase):
self._assert_status_code_is(page_response_2, 400)
self._assert_error_code_is(page_response_2, error_codes.USER_SLUG_DUPLICATE)
def test_cannot_create_page_with_invalid_content_format(self):
page_request = self._test_page_payload(slug="mypageinvalidformat")
page_request["content_format"] = "xml"
page_response_1 = self._post("pages", page_request)
self._assert_status_code_is(page_response_1, 400)
self._assert_error_code_is(page_response_1, error_codes.USER_REQUEST_INVALID_PARAMETER)
def test_page_requires_name(self):
page_request = self._test_page_payload(slug="requires-name")
del page_request['title']
@@ -89,16 +102,30 @@ class PageApiTestCase(BasePageApiTestCase):
self._assert_status_code_is(page_response, 400)
self._assert_error_code_is(page_response, error_codes.MALFORMED_ID)
def test_400_on_invalid_id_encoding_markdown(self):
page_request = self._test_page_payload(slug="invalid-id-encding-markdown", content_format="markdown")
page_request["content"] = '''```galaxy\nhistory_dataset_display(history_dataset_id=badencoding)\n```\n'''
page_response = self._post("pages", page_request)
self._assert_status_code_is(page_response, 400)
self._assert_error_code_is(page_response, error_codes.MALFORMED_ID)
def test_400_on_invalid_embedded_content(self):
dataset_populator = DatasetPopulator(self.galaxy_interactor)
valid_id = dataset_populator.new_history()
page_request = self._test_page_payload(slug="invalid-id-encding")
page_request = self._test_page_payload(slug="invalid-embed-content")
page_request["content"] = '''<p>Page!<div class="embedded-item" id="CoolObject-%s"></div></p>''' % valid_id
page_response = self._post("pages", page_request)
self._assert_status_code_is(page_response, 400)
self._assert_error_code_is(page_response, error_codes.USER_REQUEST_INVALID_PARAMETER)
assert "embedded HTML content" in page_response.text
def test_400_on_invalid_markdown_call(self):
page_request = self._test_page_payload(slug="invalid-markdown-call", content_format="markdown")
page_request["content"] = '''```galaxy\njob_metrics(job_id)\n```\n'''
page_response = self._post("pages", page_request)
self._assert_status_code_is(page_response, 400)
self._assert_error_code_is(page_response, error_codes.MALFORMED_CONTENTS)
def test_show(self):
response_json = self._create_valid_page_with_slug("pagetoshow")
show_response = self._get("pages/%s" % response_json['id'])
@@ -108,6 +135,7 @@ class PageApiTestCase(BasePageApiTestCase):
self.assertEqual(show_json["slug"], "pagetoshow")
self.assertEqual(show_json["title"], "MY PAGE")
self.assertEqual(show_json["content"], "<p>Page!</p>")
self.assertEqual(show_json["content_format"], "html")
def test_403_on_unowner_show(self):
response_json = self._create_valid_page_as("others_page_show@bx.psu.edu", "otherspageshow")
templates/webapps/galaxy/dataset/display.mako
+3 -1
View File
@@ -71,8 +71,10 @@
%endif
## TODO: why is the default font size so small?
<pre style="font-size: 135%">${ data_to_render | h }</pre>
%elif data.get_size() == 0:
<i>Dataset is empty.</i>
%else:
<p align='center'>Cannot show dataset content</p>
<i>Problem displaying dataset content.</i>
%endif
</%def>
templates/webapps/galaxy/page/display_markdown.mako
+30
View File
@@ -0,0 +1,30 @@
<%inherit file="/display_base.mako"/>
<%def name="javascript_app()">
${parent.javascript_app()}
<script type="text/javascript">
config.addInitialization(function() {
console.log("page/display_markdown.mako, javascript_app", "Setup page display markdown");
window.bundleEntries.mountPageDisplay();
});
</script>
</%def>
<%def name="stylesheets()">
${parent.stylesheets()}
${h.css( "base" )}
</%def>
<%def name="render_item_header( item )">
## No header for pages.
</%def>
<%def name="render_item_links( page )">
</%def>
<%def name="render_item( page, page_data=None )">
<div id="page-display-content" page_id="${page_data}">
</div>
</%def>
test/integration/test_page_revision_json_encoding.py
+35 -5
View File
@@ -18,23 +18,53 @@ class PageJsonEncodingIntegrationTestCase(integration_util.IntegrationTestCase):
def setUp(self):
super(PageJsonEncodingIntegrationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.history_id = self.dataset_populator.new_history()
def test_page_encoding(self):
history_id = self.dataset_populator.new_history()
request = dict(
slug="mypage",
title="MY PAGE",
content='''<p>Page!<div class="embedded-item" id="History-%s"></div></p>''' % history_id,
content='''<p>Page!<div class="embedded-item" id="History-%s"></div></p>''' % self.history_id,
)
page_response = self._post("pages", request)
api_asserts.assert_status_code_is_ok(page_response)
sa_session = self._app.model.context
page_revision = sa_session.query(model.PageRevision).all()[0]
page_revision = sa_session.query(model.PageRevision).filter_by(content_format="html").all()[0]
assert '''id="History-1"''' in page_revision.content, page_revision.content
assert '''id="History-%s"''' % history_id not in page_revision.content, page_revision.content
assert '''id="History-%s"''' % self.history_id not in page_revision.content, page_revision.content
show_page_response = self._get("pages/%s" % page_response.json()["id"])
api_asserts.assert_status_code_is_ok(show_page_response)
content = show_page_response.json()["content"]
assert '''id="History-1"''' not in content, content
assert '''id="History-%s"''' % history_id in content, content
assert '''id="History-%s"''' % self.history_id in content, content
def test_page_encoding_markdown(self):
dataset = self.dataset_populator.new_dataset(self.history_id)
dataset_id = dataset["id"]
request = dict(
slug="mypage-markdown",
title="MY PAGE",
content='''```galaxy
history_dataset_display(history_dataset_id=%s)
```''' % dataset["id"],
content_format="markdown",
)
page_response = self._post("pages", request)
api_asserts.assert_status_code_is_ok(page_response)
sa_session = self._app.model.context
page_revision = sa_session.query(model.PageRevision).filter_by(content_format="markdown").all()[0]
assert '''```galaxy
history_dataset_display(history_dataset_id=1)
```''' in page_revision.content, page_revision.content
assert '''::: history_dataset_display history_dataset_id=%s''' % dataset_id not in page_revision.content, page_revision.content
show_page_response = self._get("pages/%s" % page_response.json()["id"])
api_asserts.assert_status_code_is_ok(show_page_response)
content = show_page_response.json()["content"]
assert '''```galaxy
history_dataset_display(history_dataset_id=1)
```''' not in content, content
assert '''```galaxy
history_dataset_display(history_dataset_id=%s)
```''' % dataset_id in content, content
test/unit/test_markdown_validate.py
+14
View File
@@ -36,6 +36,20 @@ printf('hello')
job_metrics(job_id=THISFAKEID)
```
""")
# assert multiple valid container is fine.
assert_markdown_valid("""
```galaxy
job_metrics(job_id=THISFAKEID)
```
Markdown between directives.
```galaxy
job_metrics(job_id=THISFAKEID)
```
""")
# assert valid container is fine at end of document.
assert_markdown_valid("""
```galaxy